Hi Raihan, If you press Help on the Alphafold tool dialog it will show the documentation, including the answers to most of your questions. If you actually used "predict" then it uses ColabFold which is an optimized version of AlphaFold2, as it says here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> If you used alphafold fetch or search, it just gets the most similar sequence from the AlphaFold database: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#match> I don't know the specific reasons for the difference in your structure, but there are different parameters for running alphafold2, which may have been different between the two, and other differences in ColabFold vs. AlphaFold2. You would have to read all the details given at the Alphafold Database to see what parameters they used, look at the parameters you used with the prediction run on ColabFold using the ChimeraX tool, as well as the Colabfold paper to see what might be different. Regarding the structures themselves, probably you should pay more attention to which parts have higher confidence scores (pLDDT as shown with the ribbon coloring when you predict or fetch alphafold structures with ChimeraX). The specific conformations of any parts with low confidence are not that meaningful anyway. The coloring is explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#coloring> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2024, at 2:10 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi! Greetings. I hope you’re doing well. Recently, I did a structure prediction of a protein using the built-in AlphaFold of ChimeraX. Also, I downloaded the predicted structure of the same protein from the AF database. Surprisingly, when I superimposed these two structures, I found that they were pretty structurally different. However, the sequences are entirely similar. Could you please tell me what the reason for this is? And, is the built-in AlphaFold the AlphaFold2 or AlphaFold3? Thank you.
Regards, Raihan